Fig. 3

Gene expression analysis of 3D-cultured vascular endothelial cells following SARS-CoV-2 infection and LPA treatment. (A) Venn diagram of differentially expressed genes (DEGs) in vascular endothelial cells (HMVEC-Lung), comparing SARS-CoV-2 infection with control treatment (Cont) and LPA treatment with SARS-CoV-2 infection (FDR P < 0.05, fold change < 1.5). (B) Volcano plot showing upregulated (red) and downregulated (green) DEGs upon SARS-CoV-2 infection (left) and LPA treatment (right) in HMVEC-Lung. Purple spots indicate upregulated genes, and blue spots indicate downregulated genes when comparing SARS-CoV-2 with the control. (C) The k-means clustering analysis revealed 8 clusters in the 2,000 most variable genes in HMVEC-L. Pathway analysis of 116 genes in cluster 2 referred to GO biological processes and KEGG pathways. Transcriptional changes are heatmapped from green (strongly downregulated) to red (highly upregulated). Permission has been obtained from Kanehisa laboratories for using KEGG pathway database⁴². (D) Pathway analysis using KEGG database. A heatmap showing the activation of significantly enriched pathways, comparing SARS-CoV-2 infection with LPA treatment in HMVEC-Lung, HBMEC, and HRGEC. Pathways related to TNF signaling (highlighted in blue) and IL-17 signaling (highlighted in red) are shown. Enrichment values [-log(p-value)] are scaled from 0 to 1 (green to red). Permission has been obtained from Kanehisa laboratories for using KEGG pathway database⁴².